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Diverse Diazotrophs Are Present on Sinking Particles in the North Pacific

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Diverse Diazotrophs Are Present on Sinking Particles in the North Pacific The ISME Journal https://doi.org/10.1038/s41396-018-0259-x ARTICLE Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre 1,2 1 3 4 4,5,6 Hanna Farnelid ● Kendra Turk-Kubo ● Helle Ploug ● Justin E. Ossolinski ● James R. Collins ● 4 1 Benjamin A. S. Van Mooy ● Jonathan P. Zehr Received: 29 March 2018 / Revised: 3 July 2018 / Accepted: 26 July 2018 © The Author(s) 2018. This article is published with open access Abstract Sinking particles transport carbon and nutrients from the surface ocean into the deep sea and are considered hot spots for bacterial diversity and activity. In the oligotrophic oceans, nitrogen (N2)-fixing organisms (diazotrophs) are an important source of new N but the extent to which these organisms are present and exported on sinking particles is not well known. Sinking particles were collected every 6 h over a 2-day period using net traps deployed at 150 m in the North Pacific Subtropical Gyre. The bacterial community and composition of diazotrophs associated with individual and bulk sinking particles was assessed using 16S rRNA and nifH gene amplicon sequencing. The bacterial community composition in bulk 1234567890();,: 1234567890();,: particles remained remarkably consistent throughout time and space while large variations of individually picked particles were observed. This difference suggests that unique biogeochemical conditions within individual particles may offer distinct ecological niches for specialized bacterial taxa. Compared to surrounding seawater, particle samples were enriched in different size classes of globally significant N2-fixing cyanobacteria including Trichodesmium, symbionts of diatoms, and the unicellular cyanobacteria Crocosphaera and UCYN-A. The particles also contained nifH gene sequences of diverse non- cyanobacterial diazotrophs suggesting that particles could be loci for N2 fixation by heterotrophic bacteria. The results demonstrate that diverse diazotrophs were present on particles and that new N may thereby be directly exported from surface waters on sinking particles. Introduction Marine environments exhibit microscale gradients of organic carbon and nutrients, representing diverse micro- Electronic supplementary material The online version of this article niches for microorganisms to exploit. Particulate organic (https://doi.org/10.1038/s41396-018-0259-x) contains supplementary material, which is available to authorized users. matter (POM) is ubiquitous in seawater and composed of a mixture of living microorganisms and dead detrital matter, * Hanna Farnelid providing ‘hotspots’ for microbial activity and organic [email protected] matter remineralization that significantly contribute to bio- 1 Ocean Sciences Department, University of California at Santa geochemical element cycling rates [1]. Sinking particles Cruz, Santa Cruz, CA, USA transport organic and inorganic material into the deep ’ 2 Centre for Ecology and Evolution in Microbial Model Systems, ocean, a process known as the ocean s biological pump [2]. Linnaeus University, Kalmar, Sweden Because of their importance, sinking particles and the 3 Department of Marine Sciences, University of Gothenburg, composition and function of their associated community is Gothenburg, Sweden receiving increasing interest [3–5]. Compared to larger 4 Department of Marine Chemistry & Geochemistry, Woods Hole phytoplankton, the representation of picoplankton in sink- Oceanographic Institution, Woods Hole, MA, USA ing particles has generally been thought to be negligible due 5 MIT/WHOI Joint Program in Oceanography, University of to their small size, slow sinking velocity and tight regulation Washington, Seattle, WA, USA through grazing [6]. However, in recent years the possibility 6 School of Oceanography and eScience Institute, University of of export of small picoplankton through incorporation into Washington, Seattle, WA, USA aggregates or fecal pellets has been increasingly recognized H. Farnelid et al. [7, 8] and has been proposed to be in proportion to their while UCYN-B (Crocosphaera sp.) can be found free- total net primary production [9, 10]. living but may also form colonies, aggregates or live in The bacterial community composition of particulate symbiosis with a diatom [26]. The physiology of the material has been assessed in several different environ- broadly defined UCYN-C group is still largely unknown. ments, suggesting that particle attached communities are To explore diazotroph diversity, the nifH gene, a gene phylogenetically distinct from that of the surrounding water encoding a subunit of the nitrogenase enzyme, has been (e.g., [5, 11–13]). Groups that are enriched on sinking frequently used. In recent years nifH gene sequences related particles include members of Bacteroidetes, Planctomy- to non-cyanobacterial, heterotrophic diazotrophs have been cetes, and Roseobacter [3, 14]. Since particles are thought reported from various oligotrophic ocean regions [27, 28]. to represent diverse microscale conditions, bulk analyses of How heterotrophic diazotrophs support N2 fixation in the sedimented or size fractionated material may not provide oxygenated surface ocean is not yet understood and the high-resolution insights into the associated communities of significance to global N2 fixation rates is debated [29, 30]. It individual particles. In addition, only few studies have has been proposed that heterotrophic N2 fixation may take considered degradation dynamics during sample collection place in close association with phytoplankton or within [15]. Thus, molecular characterization of individual parti- interiors of particles but this has not yet been resolved [29]. cles collected during short time scales may provide novel Sinking particles constitute a diverse spectrum of envir- insights into the composition of sinking particles. onments for their colonizers based on the history of the The North Pacific Subtropical Gyre (NPSG) is char- organic matter by which they are formed. Low O2 con- acterized by low concentrations of macronutrients and centrations within sinking particles and aggregates due to warm surface water temperatures. The ecosystem is domi- microbial remineralization of organic matter have pre- nated by relatively low rates of primary production and low viously been reported [31, 32]; these microenvironments particulate organic carbon (POC) flux at the base of the would be potential niches for O2-sensitive diazotrophs. In euphotic zone [16]. Primary production in the NPSG is this study, we investigate the bacterial composition and the limited by nitrogen (N) and the dissolved dinitrogen gas associated populations of diazotrophs on both individually (N2) is only available to N2-fixing organisms (diazotrophs), picked and bulk samples of sinking particles in the NPSG, which can reduce N2 into bioavailable ammonium. In the and compare the community composition with that of the NPSG, diazotrophs contribute to a significant portion surrounding seawater. Using high-throughput nifH gene (26–47% during the years 2006–2013) of particulate nitro- amplicon sequencing we also investigate whether diazo- gen export [17]. However, the fate of the newly fixed N2 in troph biomass is exported on sinking particles and if par- the marine food web is not fully understood and the extent ticles could be potential loci for heterotrophic N2 fixation in to which cells of dead or living N2-fixing organisms are the oligotrophic ocean. exported from the euphotic zone on sinking particles may vary among the diverse species [18, 19]. In the oligotrophic open ocean, significant diazotrophs associated with larger Methods size fractions of plankton include the widely distributed filamentous N2-fixing cyanobacterium Trichodesmium [20] Sample collection at sea and heterocystous-cyanobacterial endosymbionts of dia- toms [21]. While diatoms can be exported directly due to Lagrangian sampling was performed during the HOE- their relatively heavy silicified cell walls [22] Tricho- Legacy 2B cruise (KOK1507) in the NPSG onboard the R/ desmium has been suggested to have low direct export VKa’imikai-O-Kanaloa in an anticyclonic eddy (Fig. 1). efficiency [23]. Small unicellular cyanobacterial diazo- Water column properties (0–200 m) were determined from trophs (UCYN), are also highly prevalent (e.g., [24]) and vertical depth profiles using a rosette of Niskin bottles may consequently play a significant role in POC export, but equipped with a fluorometer and temperature, conductivity little is known about their possible export mechanisms. and oxygen sensors every 4 h during 25 July to 3 August N2 fixation is an energy demanding and oxygen (O2) 2015. Surface-tethered particle net traps with a diameter of sensitive process. Cyanobacterial diazotrophs have various 1.25 m (1.23 m2 area of collection) and a 20 µm mesh cod mechanisms for protecting the nitrogenase enzyme from end [33] were deployed at 150 m for ~5–6 h. A total of 7 inactivation by O2 including temporal separation of N2 deployments (Fig. 1,D1–D7) were conducted over a 48 h fixation and photosynthesis, heterocyst formation, and period (Table S1). An acoustic release was used to close the symbiotic interactions. The unicellular cyanobacterial dia- traps prior to recovery so that material from the overlying zotrophs (UCYN-A, UCYN-B and UCYN-C) exhibit a water column was not inadvertently sampled. Traps were range of cellular strategies and interactions [25]. UCYN-A recovered immediately upon closure, except in the case of lives in association with a photosynthetic picoeukaryote,
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